Revealing the Folding of Single-Chain Polymeric Nanoparticles at the Atomistic Scale by Combining Computational Modeling and X-ray Scattering

Predicting 3D structures of synthetic heterograft polymers in solution starting from a chemical structure remains a great challenge. Here, we get grip on the 3D structures formed by amphiphilic, random heterograft polymers in water depending on the nature of the hydrophilic graft. Atomistic MD simulations in explicit water on a μs time scale show that large Jeffamine-based grafts combined with randomly distributed hydrophobic grafts induce the formation of worm-like structures with local hydrophobic domains. Replacing Jeffamine by glucose affords core-shell ellipsoidal structures. The simulated small-angle X-ray scattering (SAXS) curves from the simulation results show excellent agreement with experimental SAXS results for the Jeffamine-based copolymers. For the glucose-based copolymers, the experimental SAXS results also indicated the presence of core-shell structures, albeit that (some) multichain aggregation was present. Our work highlights that global conformations of very large heterograft polymers (up to ∼30,000 atoms) can now be studied with (accelerated) MD simulations at the atomic scale in solvent (up to 2.5 million atoms). This joint approach constitutes a reliable tool to understand the folding and possible aggregation behavior of heterograft polymers in solution, paving the way toward predictive modeling of nanoparticle structures from a polymer's chemical structure.

High Molecular Weight Uniform Polymers Encoding Octal Sequences by Passerini Iterative Exponential Growth

Sequence-defined polymers composed of a large pool of chemically distinct monomers (SDPs) have been pursued to achieve the structural and functional precisions exhibited by biopolymers in nonbiological environments. In contrast to the incremental growth of SDPs by sequential addition of individual monomers, the iterative exponential growth (IEG) method allows the synthesis of high molecular-weight SDPs, but their sequences have been composed mostly of binary monomers. Consequently, achieving high molecular-weight SDPs built with a large pool of monomers remains a challenge. Here we report the Passerini iterative exponential growth (P-IEG) approach that enables efficient synthesis of 128-mer uniform poly(hydroxybutyrate) (PHB), possessing 127 γ-acylamino cyclohexyl side groups (27 kDa, Đ = 1) and a 31-mer SDP, encoding an octal sequence composed of eight chemically distinct repeating units. Taking advantage of the combinatorial character of the Passerini three-component reaction involving an aldehyde, a carboxylic acid, and an isocyanide to form an acyloxy amide linkage, we simultaneously achieved the exponential chain growth through the convergence of bifunctional building blocks and side-chain implementation by selecting appropriate isocyanides as a third component. The P-IEG approach enabled the synthetic encoding of complex information, an octal sequence equivalent to a 93-bit binary code, into a 31-mer SDP. Our proposed P-IEG method could contribute to the synthesis of synthetic macromolecules with absolutely defined sequences of functionalities. These polymers could be used for the development of functional materials with properties not achievable by conventional polymers, including polymers storing digital information at higher density.

Chain stretching in brushes favors sequence recognition for nucleobase-functionalized flexible precise oligomers

Six different flexible stereocontrolled oligo(triazole-urethane)s substituted by precise sequences of nucleobases or analogs are synthesized. Molecular dynamics simulations indicate that the flexibility of the backbone leads to unspecific complexation of pairs of oligomers, irrespective of the complementarity of their sequences. This is ascribed to the existence of other interactions between pairs of oligomers, as well as to the spatial blurring of the sequence order encoded in the chemical structure of the chain due to its flexibility. The same conclusions are drawn when investigating the irreversible adsorption of different probe oligomers onto a layer of target oligomers grafted by click chemistry in a mushroom configuration on a silicon substrate. In contrast, when the target oligomers are grafted in denser brush configurations, irreversible adsorption becomes more specific, with it being twice as probable that probe chains of complementary sequence would be irreversibly-bound to the layer of target chains than those of non-complementary sequence. This is ascribed to lateral excluded volume interactions between chains in the brush, leading to partial chain stretching and increased spatial preservation of the information contained in the monomer sequence of the chains. At even higher grafting densities, however, the penetration of the probe chains in the brush becomes increasingly difficult, resulting in a loss of binding efficiency. Our work thus demonstrates the adverse role of chain flexibility in the specificity of complexation between nucleobase-functionalized oligomers and provides directions for an improvement of specificity by tuning the grafting density of target chains on a substrate.

Revealing the Effect of Stereocontrol on Intermolecular Interactions between Abiotic, Sequence-Defined Polyurethanes and a Ligand

The development of precision polymer synthesis has facilitated access to a diverse library of abiotic structures wherein chiral monomers are positioned at specific locations within macromolecular chains. These structures are anticipated to exhibit folding characteristics similar to those of biotic macromolecules and possess comparable functionalities. However, the extensive sequence space and numerous variables make selecting a sequence with the desired function challenging. Therefore, revealing sequence-function dependencies and developing practical tools are necessary to analyze their conformations and molecular interactions. In this study, we investigate the effect of stereochemistry, which dictates the spatial location of backbone and pendant groups, on the interaction between sequence-defined oligourethanes and bisphenol A ligands. Various methods are explored to analyze the receptor-like properties of model oligomers and the ligand. The accuracy of molecular dynamics simulations and experimental techniques is assessed to uncover the impact of discrete changes in stereochemical arrangements on the structures of the resulting complexes and their binding strengths. Detailed computational investigations providing atomistic details show that the formed complexes demonstrate significant structural diversity depending on the sequence of stereocenters, thus affecting the oligomer-ligand binding strength. Among the tested techniques, the fluorescence spectroscopy data, fitted to the Stern-Volmer equation, are consistently aligned with the calculations, thus validating the developed simulation methodology. The developed methodology opens a way to engineer the structure of sequence-defined oligomers with receptor-like functionality to explore their practical applications, e.g., as sensory materials.

Dynamic self-assembly of supramolecular catalysts from precision macromolecules

We show the emergence of strong catalytic activity at low concentrations in dynamic libraries of complementary sequence-defined oligomeric chains comprising pendant functional catalytic groups and terminal recognition units. In solution, the dynamic constitutional library created from pairs of such complementary oligomers comprises free oligomers, self-assembled di(oligomeric) macrocycles, and a virtually infinite collection of linear poly(oligomeric) chains. We demonstrate, on an exemplary catalytic system requiring the cooperation of no less than five chemical groups, that supramolecular di(oligomeric) macrocycles exhibit a catalytic turnover frequency ca. 20 times larger than the whole collection of linear poly(oligomers) and free chains. Molecular dynamics simulations and network analysis indicate that self-assembled supramolecular di(oligomeric) macrocycles are stabilized by different interactions, among which chain end pairing. We mathematically model the catalytic properties of such complex dynamic libraries with a small set of physically relevant parameters, which provides guidelines for the synthesis of oligomers capable to self-assemble into functionally-active supramolecular macrocycles over a larger range of concentrations.

Revealing the Organization of Catalytic Sequence-Defined Oligomers via Combined Molecular Dynamics Simulations and Network Analysis

Similar to biological macromolecules such as DNA and proteins, the precise control over the monomer position in sequence-defined polymers is of paramount importance for tuning their structures and properties toward achieving specific functions. Here, we apply molecular network analysis on three-dimensional structures issued from molecular dynamics simulations to decipher how the chain organization of trifunctional catalytic oligomers is influenced by the oligomer sequence and the length of oligo(ethylene oxide) spacers. Our findings demonstrate that the tuning of their primary structures is crucial for favoring cooperative interactions between the catalytic units and thus higher catalytic activities. This combined approach can assist in establishing structure-property relationships, leading to a more rational design of sequence-defined catalytic oligomers via computational chemistry.

Discrete oligourethanes of sequence-regulated properties – impact of stereocontrol

Properties and functions of natural biopolymers such as proteins are strongly dependent on the sequence of amino acid monomers. The regulation of the properties of synthetic polymers by controlling monomer...

Easily Functionalized and Readable Sequence-Defined Polytriazoles

Developing sequence-defined skeletons that could be conveniently characterized and functionalized with diverse side groups is attractive but challenging. Here we report one novel sequence-defined polytriazole structure bearing side groups at its triazole rings. Its construction was facilely accessed by the iterative employments of azidation and iridium-catalyzed cycloaddition of azide with internal 1-thioalkyne (IrAAC) in solution phase. The easy preparation of 1-thioalkyne monomers and the excellent tolerance of IrAAC enable the introduction of diverse functional side chains to this architecture. The obtained sequence was effectively characterized by tandem mass spectrometry owing to the efficient fractures of both of the Csp³-S and Csp³-N bonds in its backbone, indicating its potential utilization in high-capacity digital polymer developments. Further successful application of this structure in building monodisperse macromolecules exhibiting aggregation-induced emission (AIE) characteristics demonstrates its expected application in functional material fabrications.

Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends

In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.

IrAAC-based construction of dual sequence-defined polytriazoles

One novel dual sequence-defined polytriazole structure was facilely achieved through an IrAAC-based iterative sequential growth strategy.

Regulation of tectonic sequences in chain-folding-directed monodisperse isomeric oligomers precisely tailored by Ugi-hydrosilylation orthogonal cycles

Monodisperse discrete oligomers with a tailored sequence of linkages within their backbones, which has been defined as a tectonic sequence, were precisely constructed through Ugi-4CRs coupled to hydrosilylation orthogonal cycles.

1,2,3-Triazole-based sequence-defined oligomers and polymers

This review offers a summary on the advances in the construction of 1,2,3-triazole-based sequence-defined oligomers and polymers through MAAC-based ISG or IEG strategies.

Using nickel to fold discrete synthetic macromolecules into single-chain nanoparticles

Sequence-defined macromolecules were prepared with a thiolactone-based platform whereby ligand functionalities were introduced along the backbone enabling a nickel induced formation of single-chain nanoparticles.

Sequence-defined l-glutamamide oligomers with pendant supramolecular motifs via iterative synthesis and orthogonal post-functionalization

One of the great challenges in polymer chemistry is to achieve discrete and sequence-defined synthetic polymers that fold in defined conformations and form well-defined three-dimensional structured particles.